Matthew Cook

Matthew Cook is working on the development of a vaccine to help Tasmanian growers manage amoebic gill disease in Atlantic salmon.

Dr Mathew Cook: developing molecular tools for Atlantic salmon aquaculture

Dr Mathew Cook leads research developing molecular tools to support the health and productivity of Australia's Atlantic salmon industry.

  • 13 August 2007 | Updated 14 October 2011

Current activities

Dr Mathew Cook is a molecular immunologist and geneticist. He works on aquaculture research with CSIRO Marine and Atmospheric (CMAR) and the Food Futures Flagship (FFF).

Dr Cook leads research on the development of a vaccine against amoebic gill disease (AGD), a major health concern for Tasmania’s Atlantic salmon industry that is caused by a parasitic amoeba that attaches to the salmons' gills.

The AGD vaccine project has:

  • identified genes in the amoeba that represent the most logical vaccine candidates, and incorporated these in experimental vaccines
  • tested the experimental vaccines in laboratory trials in collaboration with the University of Tasmania, Hobart, Tasmania, Australia
  • achieved a 40 per cent increase in protection against AGD.

The selected vaccine is now being tested under commercial conditions.

The experimental vaccine has achieved a 40 per cent increase in protection against amoebic gill disease.

Dr Cook's other research involves:

  • developing molecular markers for AGD resistance
  • investigating sex determination and the application of sex ratio manipulation in Atlantic salmon
  • providing advice and assistance on AGD and related fish health issues for an Atlantic salmon selective breeding program.

Much of this research takes place with the support and cooperation of Tasmania’s Atlantic salmon industry.


Before joining CSIRO in 2002, Dr Cook taught biology, invertebrate and vertebrate zoology, anatomy and physiology and ecology at the University of South Australia in Adelaide.

Academic qualifications

Dr Cook completed a Bachelor of Environmental Toxicology with Honours at the University of South Australia.

His Doctorate, with the University of Adelaide’s School of Pharmaceutical, Molecular and Biomedical Sciences, investigated the modulation of phagocyte (a type of white blood cell) activity in cultured snapper.


In 2004, Dr Cook was one of 30 scientists Australia-wide funded to work overseas under the Young Australian Researchers Program, a federal Government initiative conducted by the Australian Academy of Science.

Dr Cook worked with Dr Bjorn Hoyheim of the Norwegian School of Veterinary Science in Oslo, Norway, leader of the European Salmon Genome Project.

He made use of a unique and comprehensive Atlantic salmon DNA microarray to investigate gene activation during the salmon’s immune response to AGD.

Dr Cook is active in postgraduate supervision and is a reviewer for several scientific journals on immunology and aquaculture.

Read more about the vaccine for amoebic gill disease in Atlantic salmon.